ELM - Detail for DEG_Cend_DCAF12

Accession:	ELME000560
Functional site class:	DCAF12 C-terminal diGlu degrons
Functional site description:	DCAF12 degrons bind to its WD40 repeat domain through their C-terminal di-glutamate motif (Pla-Prats,2023). CCT5 is a subunit of the TRiC chaperonin carrying the C-terminal double glutamate motif. DCAF12 uses a positively charged pocket at the centre of the WD40 β‐propeller to bind the C‐terminus of CCT5. This domain:motif interaction established primarily via H-bonding and salt bridging has been characterized by cryo-electron microscopy in atomic detail (8AJM; Pla-Prats,2023).
ELM Description:	Two Cul4 E3 ubiquitin ligase complexes, Cul4TRPC4AP and Cul4DCAF12, have been identified as targeting C-terminal degrons (Koren,2018). The DCAF12 substrate-recognition subunit of Cullin-4 ubiquitin ligases is responsible for the recognition of the terminal di-glutamate degrons through its WD40 repeat domain (Pla-Prats,2023). Two structures were solved revealing the binding between TCPE_HUMAN(P48643) and DCA12_HUMAN (Q5T6F0). In the structure (8AJM), the binding pocket of the domain is flanked with positively charged residues, locking down Glu at the -2 position with hydrogen bonds and a double salt bridge to Arg203 and His144, while Glu at -1 can also engage these positive patches(8AJM). Inspecting (8AJO) reveals the precisely coordinated COO- via double salt bridge to Arg256. Hydrogen bonds with the pocket are also formed at -3 and -4 positions. Position -5 exits the pocket and is largely disordered (Pla-Prats,2023). Most of the well-characterized instances have C-termini natively ending in Glu-Glu, although generation of the same site through proteolysis cannot be excluded. The degron residues are rather strict: DCAF12’s WD40 repeats demand a glutamic acid at the −2 position (Timms,2020). Nevertheless, there is some flexibility in the specific residue at the C-terminal (-1) position. Although DCAF12 prefers a twin C-terminal glutamic acid (−EE) motif, other residues are also tolerated to some extent. In addition, a glutamate in the -4 position forming an H-bond with the DCAF12 backbone is also visible, raising the possibility of extending the degron motif from “EE$” to “..EE$”. Several members of the melanoma antigen gene (MAGE) family, usually expressed only in the male germline but aberrantly expressed in cancers to drive tumorigenesis, have the −EE$ motif. DCAF12-mediated degradation of MAGEA3 and MAGEA6 through their C-terminal −EE$ motifs is crucial for inducing autophagy in response to nutrient deprivation (Ravichandran,2019).
Pattern:	`..EE$`
Pattern Probability:	`0.0000142`
Present in taxon:	Metazoa
Interaction Domain:	WD40 repeat (IPR001680) WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide (Stochiometry: 1 : 1)

DCAF12 C-terminal diGlu degrons

DCAF12 degrons bind to its WD40 repeat domain through their C-terminal di-glutamate motif (Pla-Prats,2023). CCT5 is a subunit of the TRiC chaperonin carrying the C-terminal double glutamate motif. DCAF12 uses a positively charged pocket at the centre of the WD40 β‐propeller to bind the C‐terminus of CCT5. This domain:motif interaction established primarily via H-bonding and salt bridging has been characterized by cryo-electron microscopy in atomic detail (8AJM; Pla-Prats,2023).

ELM Description:

Two Cul4 E3 ubiquitin ligase complexes, Cul4TRPC4AP and Cul4DCAF12, have been identified as targeting C-terminal degrons (Koren,2018). The DCAF12 substrate-recognition subunit of Cullin-4 ubiquitin ligases is responsible for the recognition of the terminal di-glutamate degrons through its WD40 repeat domain (Pla-Prats,2023). Two structures were solved revealing the binding between TCPE_HUMAN(P48643) and DCA12_HUMAN (Q5T6F0). In the structure (8AJM), the binding pocket of the domain is flanked with positively charged residues, locking down Glu at the -2 position with hydrogen bonds and a double salt bridge to Arg203 and His144, while Glu at -1 can also engage these positive patches(8AJM). Inspecting (8AJO) reveals the precisely coordinated COO- via double salt bridge to Arg256. Hydrogen bonds with the pocket are also formed at -3 and -4 positions. Position -5 exits the pocket and is largely disordered (Pla-Prats,2023). Most of the well-characterized instances have C-termini natively ending in Glu-Glu, although generation of the same site through proteolysis cannot be excluded. The degron residues are rather strict: DCAF12’s WD40 repeats demand a glutamic acid at the −2 position (Timms,2020). Nevertheless, there is some flexibility in the specific residue at the C-terminal (-1) position. Although DCAF12 prefers a twin C-terminal glutamic acid (−EE) motif, other residues are also tolerated to some extent. In addition, a glutamate in the -4 position forming an H-bond with the DCAF12 backbone is also visible, raising the possibility of extending the degron motif from “EE$” to “..EE$”. Several members of the melanoma antigen gene (MAGE) family, usually expressed only in the male germline but aberrantly expressed in cancers to drive tumorigenesis, have the −EE$ motif. DCAF12-mediated degradation of MAGEA3 and MAGEA6 through their C-terminal −EE$ motifs is crucial for inducing autophagy in response to nutrient deprivation (Ravichandran,2019).

..EE$

0.0000142

Metazoa

WD40 repeat (IPR001680) WD-40 repeats (also known as WD or beta-transducin repeats) are short ~40 amino acid motifs, often terminating in a Trp-Asp (W-D) dipeptide (Stochiometry: 1 : 1)

The genome can be subject to various types of damage, such as germline mutations, replication errors and more. The mRNA molecules can also be mis-processed or translated erroneously. In addition, protein molecules can suffer chemical damage (e.g. hydrolysis) as they age. Protein quality control is a vital cellular process that ensures the proper folding, assembly, and function of proteins. It involves various surveillance mechanisms that detect misfolded or damaged proteins and either facilitate their refolding or target them for degradation via protein degradation pathways such as the ubiquitin-proteasome system, thereby maintaining cellular homeostasis (Yeh,2021).

C-terminal degrons (C-degrons, also known as destabilizing C-terminal ends, DesCEnds) are short amino acid sequences located at the C-terminus of proteins that play a crucial role in regulating protein stability and degradation. These degrons are recognized by specific E3 ubiquitin ligases, such as the TRIM7 E3 ligase, which target the protein for ubiquitination and subsequent proteasomal degradation.

C-degron pathways have been implicated in various biological processes, including protein quality surveillance, cell cycle regulation, antiviral defense, and signal transduction. Dysregulation of C-degron pathways can lead to the accumulation of abnormal or misfolded proteins, contributing to the development of human diseases such as neurodegenerative disorders (Chen,2021).

C-terminal degrons can be present in full length proteins internally, in which case they must be activated by proteolytic cleavage. On the other hand, they can be natively present at the C-termini of other proteins or even introduced by premature translation termination.

The CUL4‐RBX1‐DDB1 (CRL4) is a highly modular family binding an activated ubiquitin enzyme via RBX1 and DDB1 adaptor protein. Various substrate receptors are recruited through DDB1, including DCAF12 (Q5T6F0). The CUL4‐RBX1‐DDB1‐DCAF12 E3 ligase recognizes proteins carrying a C-terminal di-Glutamate motif and it is linked to the transduction of pro‐apoptotic signals (Pla-Prats,2023), regulation of the Hippo pathway related to tissue growth (Cho,2020), and it also supports synaptic plasticity and function (Jiao,2022). Reporter screens identified multiple proteins degraded by DCAF12-dependent manner (Koren,2018), for example MAGA3 (P43357), playing roles in embryonal development and tumor progression. Although most proteins are recognized by the C-terminal di-Glutamate motif, some proteins targeted by DCAF12 possess poorly-characterized variant motifs lacking one of the glutamates (Lidak,2021), or bind in a completely different manner, as in the case of IAPs, where recognition of BIR domains is required (Jiao,2022).

Biological Process:
Cell Cycle Control (also annotated in these classes: )
Proteasomal Ubiquitin-Dependent Protein Catabolic Process (also annotated in these classes: )
Cellular Compartment:
Cytosol (also annotated in these classes: )
Cul4a-Ring E3 Ubiquitin Ligase Complex (also annotated in these classes: DEG_CRBN_cyclicCter_1 )
Nucleus (also annotated in these classes: )
Molecular Function:
Ubiquitin-Protein Ligase Activity (also annotated in these classes: )
Protein Domain Specific Binding (also annotated in these classes: )
Protein Binding (also annotated in these classes: )

Acc., Gene-, Name	Start	End	Subsequence	Logic	#Ev.	Organism	Notes
P22102 GART PUR2_HUMAN	1007	1010	VASGTVQLGENGKICWVKEE	TP	4	Homo sapiens (Human)
Q9NZB2 FAM120A F120A_HUMAN	1115	1118	TDSACRREAALEAAVLNKEE	TP	4	Homo sapiens (Human)
Q70CQ3 USP30 UBP30_HUMAN	514	517	FYERVLSRMQHQSQECKSEE	TP	4	Homo sapiens (Human)
P43360 MAGEA6 MAGA6_HUMAN	311	314	GGPRISYPLLHEWALREGEE	TP	2	Homo sapiens (Human)
P43357 MAGEA3 MAGA3_HUMAN	311	314	GGPHISYPPLHEWVLREGEE	TP	3	Homo sapiens (Human)
P48643 CCT5 TCPE_HUMAN	538	541	QMVRMILKIDDIRKPGESEE	TP	4	Homo sapiens (Human)	8AJM 8AJO 8AJM 8AJO

Acc., Gene-, Name

Start

End

Subsequence

Logic

#Ev.

Organism

Notes

P22102 GART
PUR2_HUMAN

1007

1010

VASGTVQLGENGKICWVKEE